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tramME (version 1.0.5)

Transformation Models with Mixed Effects

Description

Likelihood-based estimation of mixed-effects transformation models using the Template Model Builder ('TMB', Kristensen et al., 2016) . The technical details of transformation models are given in Hothorn et al. (2018) . Likelihood contributions of exact, randomly censored (left, right, interval) and truncated observations are supported. The random effects are assumed to be normally distributed on the scale of the transformation function, the marginal likelihood is evaluated using the Laplace approximation, and the gradients are calculated with automatic differentiation (Tamasi & Hothorn, 2021) . Penalized smooth shift terms can be defined using 'mgcv'.

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Version

Install

install.packages('tramME')

Monthly Downloads

3,154

Version

1.0.5

License

GPL-2

Maintainer

Balint Tamasi

Last Published

June 29th, 2023

Functions in tramME (1.0.5)

edf_smooth.tramME

EDFs of smooth shift terms
print.VarCorr.tramME

Print method for the variance-correlation parameters of a tramME object
plot.smooth.tramME

Plot smooth terms of a tramME model.
model.frame.tramME

Extract model frame from a tramME model
plot.tramME

Plotting method for tramME objects
print.anova.tramME

Printing anova.tramME table
ranef.LmME

Extract the conditional modes of random effects of an LmME model
smooth_terms.LmME

Evaluate smooth terms of a LmME model.
smooth_terms.tramME

Extract and evaluate the smooth terms of a tramME model
ranef.tramME

Point estimates and conditional variances of random effects.
print.summary.tramME

Print method for tramME model summary
print.tramME

Print tramME model
varcov

Generic method for varcov
varcov.tramME

Extract the variance-covariance matrix of the random effects
varcov.LmME

Extract the variance-covariance matrix of the random effects of an LmME model
varcov<-

Generic method for "varcov<-"
coef.LmME

Extract the coefficients of the fixed effects terms of an LmME model.
residuals.LmME

Residuals of a LmME model
coef.SurvregME

Extract the coefficients of the fixed effects terms of an SurvregME model.
residuals.tramME

Residuals of a tramME model
predict.tramME

Predict method for tramME objects
predict.tramTMB

Post-estimation calculations in a tramTMB model
summary.tramME

Summary method for tramME model
varcov<-.tramME

Set the values of the random effects covariance matrices of a tramME model.
tramTMB

Create a tramTMB object
vcov.tramME

Calculate the variance-covariance matrix of the parameters
optim_control

Set up and control optimization parameters
model.matrix.tramME

Model matrices for tramME models
sigma.LmME

Extract the SD of the error term of an LmME model.
confint.LmME

Confidence intervals for LmME model parameters
simulate.tramME

Simulate from a tramME model
variable.names.tramME

Return variable names.
tramME

General function to define and fit tramME models
vcov.LmME

Get the variance-covariance matrix of the parameters of an LmME model
VarCorr.LmME

Variances and correlation matrices of random effects of an LmME object
VarCorr.tramME

Variances and correlation matrices of random effects
BoxCoxME

Mixed-effects version of BoxCox
ColrME

Mixed-effects version of Colr
LmME

Mixed-effects version of Lm
CoxphME

Mixed-effects version of Coxph
coef.tramME

Extract the coefficients of the fixed effects terms.
LehmannME

Mixed-effects version of Lehmann
confint.tramME

Confidence intervals for tramME model parameters
PolrME

Mixed-effects version of Polr
Resp

Response objects
anova.tramME

Comparison of nested tramME models.
coef<-.tramME

Set coefficients of a tramME model.
SurvregME

Mixed-effects version of Survreg
logLik.tramME

Get the log-likelihood of the tramME model